HsaINT0095629 @ hg19
Intron Retention
Gene
ENSG00000198670 | LPA
Description
lipoprotein, Lp(a) [Source:HGNC Symbol;Acc:6667]
Coordinates
chr6:160962139-160963840:-
Coord C1 exon
chr6:160963720-160963840
Coord A exon
chr6:160962214-160963719
Coord C2 exon
chr6:160962139-160962213
Length
1506 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTGGCATGTTTTCTTTCTAGGTT
3' ss Score
10.09
Exon sequences
Seq C1 exon
CATCCTCTTCATTTGATTGTGGGAAGCCTCAAGTGGAGCCGAAGAAATGTCCTGGAAGCATTGTAGGGGGGTGTGTGGCCCACCCACATTCCTGGCCCTGGCAAGTCAGTCTCAGAACAAG
Seq A exon
GTAAGAACAGGCCCAGAAACCATCTATACTGTCCTTCCATGTAAGCCCCACAAAACCCTTCTACATTTACACAGAACCCACACAGCTGATGCATCAATACCTGCCTCTCTGTTTTCTGAAGGAGGAAAAAATATAGAAAAATTAAAAAAAGTTATATTATTATAGGTTCTCTACTTGGAAAATAGCCAAAATACAAATCTTTTTCTTGATCTGGGCAGTTCCATCAAAATCTGTAGGCACAGTGATTTGCACCAAGTTCCAATACTTTTGGAAAATATTGAAGATGCTCTGAGGGTTTCTATGGATATCCATTGTCTCACTGTCAGATGAAAAGAAAGGGAAGTTTTTAGAAATGTGACACTTTGCAGTGAGGGAGGACAAGAGCAAACTTACCTACAGTCTATCACAGGCACAGATTTTTTTTTACACTTTTGTGAATCATTGAATTCAATGCCGAGGCTATTCATCTATTCACAAACACATGAACAAATTATGGGTTGTGATCCCCATAAATGAAGAGTAATCAGTCCGAACCCACAGAACCTGGACATTTTGGGTATCGTTTCAGTGGAACATGCAATTCGTAAGTTCAGTTTGCTTGGGTGTCTCTTAGGAAGAACACATAGGACACAGACCCATCTGCCTGCATGTTTTGCTTCCTCATCTCCTTTCTACACCAGGGCACCTGTGCTCAATTGCTGTTCTCCTCTAAAGAGACTTCCTTCTGTAAGTTTGTGAAATGCCATCGACAAACCTGATCGCATCGCATTTCACTCTGCTGTTGAGTTGATTTTTCTTTACTTTATCGTTTGTAACTTCTTGCTCTACAGAGCTTTCACCTTCCACATATTTCAGATTCATTCTTTCCTAAACTGTGTGGTGGTCTATGTCCTCACTGACTATCAACATACTGCCATCATGCACTTCCTATCTCTATTCCTCTTCGTTGCAATCTGGCTCCAAGTGGCTCACACCATTATTCTGATCTATCAACTGCCTACACAGTCCTAGAAAGTAAGTGAGTCAAGAAACATCCCCCAAAAGTAAACTTTTCAGGTAAGATCAGAAGACCCTCATGAGTCACTGCTGCTCAGGATCGTATCTGGCTCCTTGAAGAGTGACCTTGCATAGATCTTGTCATAAAAAATGAAAGAGACCTTGGGAAGGTCTTGGGCTGGTCACTTTTGTCAGAGTCCAGGGCTGTGGGGTGAAAGCCACAGCTATAGAGCTTCATTCTGGAGTCACTTAGCTTTGCTCTCCTGGGGACAGGCTGTGCCTATTCTTGCCTCAGGCATCAAAAAAAGTGGCACAGATGGGCCCTTCTGAAAAATCTCACTACTGGAGCACAGCTCGAAGTTTCTACTATCCTGACGTTGGGCGGTAGTCCTTTGCTTTGGGAATATGAACATGATCAAAACTGAGTGAACTTGTCTTCCTGGCTTTCTGTACAATGAAGTAGAACAAACCATCCAATTTGACCAAAGCCTTGGCATGTTTTCTTTCTAG
Seq C2 exon
GTTTGGAAAGCACTTCTGTGGAGGCACCTTAATATCCCCAGAGTGGGTGCTGACTGCTGCTCACTGCTTGAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198670-LPA:NM_005577:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(9.3=48.8)
A:
NA
C2:
PF0008921=Trypsin=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTCATTTGATTGTGGGAAGCCT
R:
GCAGTGAGCAGCAGTCAGC
Band lengths:
183-1689
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)